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- PDB-3q3t: Alkyl Amine Renin Inhibitors: Filling S1 from S3 -

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Basic information

Entry
Database: PDB / ID: 3q3t
TitleAlkyl Amine Renin Inhibitors: Filling S1 from S3
ComponentsRenin
KeywordsHYDROLASE/HYDROLASE INHIBITOR / aspartate protease / hypertension / renin inhibitors / glycoprotein / zymogen / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


renin / juxtaglomerular apparatus development / mesonephros development / response to cGMP / renin-angiotensin regulation of aldosterone production / drinking behavior / regulation of MAPK cascade / response to immobilization stress / angiotensin maturation / amyloid-beta metabolic process ...renin / juxtaglomerular apparatus development / mesonephros development / response to cGMP / renin-angiotensin regulation of aldosterone production / drinking behavior / regulation of MAPK cascade / response to immobilization stress / angiotensin maturation / amyloid-beta metabolic process / Metabolism of Angiotensinogen to Angiotensins / cell maturation / response to cAMP / hormone-mediated signaling pathway / kidney development / insulin-like growth factor receptor binding / regulation of blood pressure / male gonad development / cellular response to xenobiotic stimulus / apical part of cell / peptidase activity / response to lipopolysaccharide / aspartic-type endopeptidase activity / signaling receptor binding / proteolysis / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Renin-like domain / Aspartic peptidase, N-terminal / A1 Propeptide / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site ...Renin-like domain / Aspartic peptidase, N-terminal / A1 Propeptide / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsWu, Z. / McKeever, B.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2011
Title: Biphenyl/diphenyl ether renin inhibitors: Filling the S1 pocket of renin via the S3 pocket.
Authors: Yuan, J. / Simpson, R.D. / Zhao, W. / Tice, C.M. / Xu, Z. / Cacatian, S. / Jia, L. / Flaherty, P.T. / Guo, J. / Ishchenko, A. / Wu, Z. / McKeever, B.M. / Scott, B.B. / Bukhtiyarov, Y. / ...Authors: Yuan, J. / Simpson, R.D. / Zhao, W. / Tice, C.M. / Xu, Z. / Cacatian, S. / Jia, L. / Flaherty, P.T. / Guo, J. / Ishchenko, A. / Wu, Z. / McKeever, B.M. / Scott, B.B. / Bukhtiyarov, Y. / Berbaum, J. / Panemangalore, R. / Bentley, R. / Doe, C.P. / Harrison, R.K. / McGeehan, G.M. / Singh, S.B. / Dillard, L.W. / Baldwin, J.J. / Claremon, D.A.
History
DepositionDec 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 31, 2021Group: Source and taxonomy / Structure summary / Category: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
Revision 2.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Renin
B: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,3258
Polymers74,5342
Non-polymers1,7916
Water2,522140
1
A: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3565
Polymers37,2671
Non-polymers1,0894
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9693
Polymers37,2671
Non-polymers7022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.253, 97.585, 148.651
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Renin / Angiotensinogenase


Mass: 37267.008 Da / Num. of mol.: 2 / Fragment: UNP residues 67-406
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: REN, renin / Plasmid: PCDNA3.1 / Cell line (production host): HEK 293 / Production host: Homo sapiens (human) / References: UniProt: P00797, renin

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Sugars , 2 types, 2 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 144 molecules

#3: Chemical ChemComp-RX0 / [(1S,3R,4S)-3-amino-4-hydroxycyclopentyl]{(3R)-3-[(1S)-1-(biphenyl-2-yl)-1-hydroxy-5-methoxypentyl]piperidin-1-yl}methanone


Mass: 480.639 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H40N2O4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.4 %
Crystal growTemperature: 278 K / Method: hanging drop
Details: 0.1 M Tris-HCl, 0.2 M ammonium sulfate, 18-26% w/v PEG3550, 5 mg/mL renin, 1 mm inhibitor, pH 7.0-8.0, HANGING DROP, temperature 278K
PH range: 7.0-8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9764
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Nov 16, 2004
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9764 Å / Relative weight: 1
ReflectionResolution: 2.6→46.359 Å / Num. obs: 24777 / % possible obs: 99 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.073 / Χ2: 1.572 / Net I/σ(I): 12.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.6-2.692.90.29222581.508192
2.69-2.83.60.26424101.448198.5
2.8-2.934.10.19924531.4561100
2.93-3.084.10.1524521.4891100
3.08-3.284.10.11624881.5681100
3.28-3.5340.08124791.5731100
3.53-3.8840.06225101.581100
3.88-4.4540.04725071.5971100
4.45-5.640.04125481.5821100
5.6-46.3593.70.04526721.88199.3

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GW5

3gw5


Resolution: 2.6→46.359 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.891 / Occupancy max: 1 / Occupancy min: 1 / SU B: 12.513 / SU ML: 0.264 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.937 / ESU R Free: 0.342 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1263 5.1 %RANDOM
Rwork0.2004 ---
obs0.2039 24725 98.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 81.37 Å2 / Biso mean: 31.43 Å2 / Biso min: 8.51 Å2
Baniso -1Baniso -2Baniso -3
1--2.22 Å20 Å20 Å2
2--3.9 Å20 Å2
3----1.68 Å2
Refinement stepCycle: LAST / Resolution: 2.6→46.359 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5164 0 124 140 5428
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225419
X-RAY DIFFRACTIONr_angle_refined_deg1.7181.9797356
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4795667
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.3424.118221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.65415856
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9411520
X-RAY DIFFRACTIONr_chiral_restr0.1160.2827
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214052
X-RAY DIFFRACTIONr_mcbond_it0.7751.53307
X-RAY DIFFRACTIONr_mcangle_it1.48225345
X-RAY DIFFRACTIONr_scbond_it2.10632112
X-RAY DIFFRACTIONr_scangle_it3.5784.52011
LS refinement shellResolution: 2.601→2.669 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 97 -
Rwork0.271 1527 -
all-1624 -
obs--90.17 %

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